The root canal morphology undergoes aging-related changes, and relevant quantitative analyses have not yet been reported. We compared the cone beam computed tomography (CBCT) and micro-computed tomography (micro-CT) scans of extracted mandibular incisors to check the accuracy of morphological measurements. Thereafter, the root canal morphology and aging-related changes in the mandibular incisors of Japanese individuals were assessed using CBCT. Six extracted teeth were fixed in a phantom head and imaged using CBCT and micro-CT. The correlation between the findings of the two imaging modalities was examined. Further, CBCT reconstructed images of the mandibular incisors of 81 individuals were observed. Age-related changes of the root canals were compared between participants aged <30 years and those aged ≥30 years. The CBCT and micro-CT findings regarding the root canals of the extracted teeth coincided in 94.4% of the cases. Mandibular incisors exhibiting two root canals in either cross-section accounted for 9.9% of central incisors and 12.4% of lateral incisors. Mandibular central incisors with two root canals were observed in two (6.3%) individuals aged <30 years and six (12.2%) aged ≥30 years. Mandibular lateral incisors with two root canals were observed in one (3.1%) individual aged <30 years and nine (18.4%) aged ≥30 years. CBCT allows accurate evaluation of complex root canal morphologies and is useful for endodontic preoperative assessment. Mandibular incisors have more frequent occurrence of two root canals with aging.